fixes #38

+PlotID/Publish.m

@@ -129,7 +129,6 @@ switch options.Method
                 sourcePath = fList{idx,'path'};
                 relativeSourcePath = strrep(sourcePath,currentPath,'');
                                 
-                %WIP relative PATh!!
                 if contains(sourcePath,{'.h5','.hdf5'}) % Linking only for HDF5
                     PlotID.createLinkedHDF5(relativeSourcePath{1,1},storPath,ID);
                 end

+PlotID/createFileCopy.m

@@ -34,7 +34,6 @@ function [storagePaths] = createFileCopy(filePaths,folderName,storPath,ID,type)
                     error([type,' is not a valid type for createFileCopy'])
             end %switch 
             
-            % Write the file
             RemotePath = fullfile(storPath,folderName, newfile);
                         
 %           Check if remote file already exists
@@ -51,7 +50,21 @@ function [storagePaths] = createFileCopy(filePaths,folderName,storPath,ID,type)
                     RemotePath = fullfile(storPath,folderName,...
                     [name(1:end-length(num2str(count))),num2str(count),ext]);
                 end
-                warning('Filename already exists in data folder');
+                [~, name, ~] = fileparts(RemotePath);
+                
+                
+                msg = ['Filename ',name,...
+                    ' already exists in the data folder' newline,...
+                    ' PlotID will add an suffix if you continue.' newline,...
+                    ' This can cause serious confusions.'];
+                warning(msg);                
+                m = input('Do you want to continue, Y/N [Y]:','s');
+                
+                if ismember(m,{'N','n'})
+                   errorMSG = ['Filename already exists in data folder.' newline,...
+                       ' Rename the File and restart PlotID.'];
+                   error();
+                end
             end
             copyfile(FileNameAndLocation,RemotePath);
             storagePaths{i} = RemotePath; 
@@ -59,6 +72,8 @@ function [storagePaths] = createFileCopy(filePaths,folderName,storPath,ID,type)
         disp([type, ' sucessfully published']);
     catch
         warning([type,' export was not sucessful'])
+    if exist('errorMSG')
+        error(errorMSG);
    end %try
 end
 

+PlotID/fileCompare.m

@@ -26,23 +26,6 @@ for i=1:height(fileList)
 
     filepath = fullfile(fileList{i,'folder'},fileList{i,'name'});
     
-
-    %% old
-    %crucial performance due to matlab bug 
-    %(see https://de.mathworks.com/matlabcentral/answers/338553-performance-of-system-dos-function)
-%     if ispc
-%         filename = ['"',filename,'"'];% Bugfix for spaces in path
-%           status = comparejava
-%         % system call that causes performance issues
-%         [status,~] = system(['fc ' filename ' ' char(filepath)]);
-%         % 0 -> identical, 1 -> not identical
-%          status = ~status; % false (not identical), true(identical)
-%                    
-%     elseif isunix %untested!
-%         [status,~] = system(['diff ' filename ' ' filepath]);
-%     else
-%         warning('Platform not supported')
-%     end
     %% comparison with java function
     % TODO test paths with spaces
     status = comparejava(filename, char(filepath));